Scaling Mesh

[Tony Kulesa]

Hi -

Is it possible to change the mesh size, such that in one compartment transport pdes are solved on a mesh of nanometer size elements, but in another compartment (which is interfaced with the first compartment via a membrane), the transport pde is solved on a mesh with micrometer size elements? 

Thanks,

Tony

[Jim Schaff]

Hi Tony,

 

In general, no it is not possible - VCell has not support for this.  The Virtual Cell uses a cartesian grid with user specified deltaX, deltaY, deltaZ which may be different, but are constants across the mesh. 

 

However, if your domain separation is along a major coordinate plane (e.g. y-z plane ... where domain1 is x<x0 and domain2 is x>=x0), and you use the MathModel interface where you directly specify the equations, then you <<MAY>> be able to rewrite the equations in domain2 (and the initial and boundary conditions) where only the "x" dimension is scaled by 0.001.    Note that VCell won't know you scaled anything, so the terms for fluxes, diffusion coefficients, reaction rates, and concentrations must be consistent, and the underlying VCell discretization of the divergence and time rate of change of concentrations must be standard (unscaled) form.

 

If you can derive such a system of equations:

1) the resulting equations may no longer be of the form that VCell can handle.

2) the simulation results would have to be rescaled.

 

VCell allows advective velocities to be independently specified in x,y,z ... but diffusion coefficients may not (isotropic only).

 

If you want to try for a particular case, we may be able to help.

 

Thanks,

 

Jim Schaff

VCell Developer